This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1f0i

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:08, 20 March 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1f0i.jpg|left|200px]]
 
-
<!--
+
==THE FIRST CRYSTAL STRUCTURE OF A PHOSPHOLIPASE D==
-
The line below this paragraph, containing "STRUCTURE_1f0i", creates the "Structure Box" on the page.
+
<StructureSection load='1f0i' size='340' side='right'caption='[[1f0i]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1f0i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_sp._PMF Streptomyces sp. PMF]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F0I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F0I FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-
{{STRUCTURE_1f0i| PDB=1f0i | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1f0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f0i OCA], [https://pdbe.org/1f0i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f0i RCSB], [https://www.ebi.ac.uk/pdbsum/1f0i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f0i ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/P84147_STRSM P84147_STRSM]
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f0/1f0i_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1f0i ConSurf].
 +
<div style="clear:both"></div>
-
'''THE FIRST CRYSTAL STRUCTURE OF A PHOSPHOLIPASE D'''
+
==See Also==
-
 
+
*[[Phospholipase D 3D structures|Phospholipase D 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
BACKGROUND: The phospholipase D (PLD) superfamily includes enzymes that are involved in phospholipid metabolism, nucleases, toxins and virus envelope proteins of unknown function. PLD hydrolyzes the terminal phosphodiester bond of phospholipids to phosphatidic acid and a hydrophilic constituent. Phosphatidic acid is a compound that is heavily involved in signal transduction. PLD also catalyses a transphosphatidylation reaction in the presence of phosphatidylcholine and a short-chained primary or secondary alcohol. RESULTS: The first crystal structure of a 54 kDa PLD has been determined to 1.9 A resolution using the multiwavelength anomalous dispersion (MAD) method on a single WO(4) ion and refined to 1.4 A resolution. PLD from the bacterial source Streptomyces sp. strain PMF consists of a single polypeptide chain that is folded into two domains. An active site is located at the interface between these domains. The presented structure supports the proposed superfamily relationship with the published structure of the 16 kDa endonuclease from Salmonella typhimurium. CONCLUSIONS: The structure of PLD provides insight into the structure and mode of action of not only bacterial, plant and mammalian PLDs, but also of a variety of enzymes as diverse as cardiolipin synthases, phosphatidylserine synthases, toxins, endonucleases, as well as poxvirus envelope proteins having a so far unknown function. The common features of these enzymes are that they can bind to a phosphodiester moiety, and that most of these enzymes are active as bi-lobed monomers or dimers.
+
[[Category: Large Structures]]
-
 
+
[[Category: Streptomyces sp. PMF]]
-
==About this Structure==
+
[[Category: Hough E]]
-
1F0I is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F0I OCA].
+
[[Category: Leiros I]]
-
 
+
[[Category: Secundo F]]
-
==Reference==
+
[[Category: Servi S]]
-
The first crystal structure of a phospholipase D., Leiros I, Secundo F, Zambonelli C, Servi S, Hough E, Structure. 2000 Jun 15;8(6):655-67. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10873862 10873862]
+
[[Category: Zambonelli C]]
-
[[Category: Phospholipase D]]
+
-
[[Category: Single protein]]
+
-
[[Category: Streptomyces sp.]]
+
-
[[Category: Hough, E.]]
+
-
[[Category: Leiros, I.]]
+
-
[[Category: Secundo, F.]]
+
-
[[Category: Servi, S.]]
+
-
[[Category: Zambonelli, C.]]
+
-
[[Category: Alpha-beta-alpha-beta-alpha structure]]
+
-
[[Category: Phospholipase d]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 15:44:46 2008''
+

Current revision

THE FIRST CRYSTAL STRUCTURE OF A PHOSPHOLIPASE D

PDB ID 1f0i

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1f0i"
Personal tools